If you’ve built a personal library of scientific papers in Mendeley, you won’t just want to delete all the data, you’ll need to export your library first, delete your account and then import it into a different tool.

Disclaimer: I’m not advocating that you delete your mendeley account (aka #mendelete), just that if you do decide to, here’s how to do it, and some alternatives to consider. Update April 2013, it wasn’t just a rumour.

Exporting your Mendeley library

Open up Mendeley Desktop, on the File menu select Export. You have a choice of three export formats:

It is probably best to create a backup in all three formats just in case as this will give you more options for importing into whatever you replace Mendeley with. Another possibility is to use the Mendeley API to export your data which will give you more control over how and what you export, or trawl through the Mendeley forums for alternatives. [update: see also comments below from William Gunn on exporting via your local SQLite cache]

Deleting your Mendeley account #mendelete

Login to Mendeley.com, click on the My Account button (top right), Select Account details from the drop down menu and scroll down to the bottom of the page and click on the link delete your account. You’ll be see a message We’re sorry you want to go, but if you must… which you can either cancel or select Delete my account and all my data. [update]To completely delete your account you’ll need to send an email to privacy at mendeley dot com. (Thanks P.Chris for pointing this out in the comments below)

Alternatives to Mendeley

Once you have exported your data, you’ll need an alternative to import your data into. Fortunately, there are quite a few to choose from [3], some of which are shown in the list below. This is not a comprehensive list, so please add suggestions below in the comments if I missed any obvious ones. Wikipedia has an extensive article which compares all the different reference management software which is quite handy (if slightly bewildering). Otherwise you might consider trying the following software:

One last alternative, if you are fed up with trying to manage all those clunky pdf files, you could just switch to Google Scholar which is getting better all the time. If you decide that Mendeley isn’t your cup of tea, now might be a good time to investigate some alternatives, there are plenty of good candidates to choose from. But beware, you may run from the arms of one large publisher (Elsevier) into the arms of another (Springer or Macmillan which own Papers and ReadCube respectively).

When I first heard about Journal Fire, I thought, Great! someone is going to take all the closed-access scientific journals and make a big bonfire of them! At the top of this bonfire would be the burning effigy of a wicker man, representing the very worst of the vanity journals [1,2].

Unfortunately Journal Fire aren’t burning anything just yet, but what they are doing is something just as interesting. Their web based application allows you to manage and share your journal club online. I thought I’d give it a whirl because a friend of mine asked me what I thought about a paper on ontologies in biodiversity [3]. Rather than post a brief review here, I’ve posted it over at Journal Fire. Here’s some initial thoughts on a quick test drive of their application:

Pros

On the up side Journal Fire:

Is a neutral-ish third party space where anyone can discuss scientific papers.

As far as I can see, Journal Fire is a small startup based in Pasadena, California. Like all startups, they might go bust. If this happens, they’ll take your journal club, and all its reviews down with them.

I think the pros mostly outweigh the cons, so if you like the idea of a third-party hosting your journal club, Journal Fire is worth a trial run.

In the last ten years, the Open Access movement has made huge progress in allowing:

“any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers.”

But there is still a long way to go yet, as much of the world’s scientific knowledge remains locked up behind publisher’s paywalls, unavailable for re-use by text-mining software and inaccessible to the public, who often funded the research through taxation.

Openly ironic?

Ironically, some of the papers that are inaccessible discuss or even champion the very Open Access movement itself. Sometimes the lack of access is deliberate, other times accidental – but the consequences are serious. Whether deliberate or accidental, restricted access to public scientific knowledge is slowing scientific progress [1]. Sometimes the best way to make a serious point is to have a laugh and joke about it. This is what the Open Access Irony Awards do, by gathering all the offenders in one place, we can laugh and make a serious point at the same time by naming and shaming the papers in question.

Serial offender and über-journal Science has an article by Elias Zerhouni on the NIH public access policy [3] (Subscribe/Join AAAS to View Full Text), another on “making data maximally available” [4] (Subscribe/Join AAAS to View Full Text) and another on a high profile advocate of open science [5] (Buy Access to This Article to View Full Text) Irony of ironies.

From Nature Publishing Group comes a fascinating paper about harnessing the wisdom of the crowds to predict protein structures [6]. Not only have members of the tax-paying public funded this work, they actually did some of the work too! But unfortunately they have to pay to see the paper describing their results. Ironic? Also, another published in Nature Medicine proclaims the “delay in sharing research data is costing lives” [1] (instant access only $32!)

From the British Medical Journal (BMJ) comes the worrying news of dodgy American laws that will lock up valuable scientific data behind paywalls [7] (please subscribe or pay below). Ironic? *

The “green” road to Open Access publishing involves authors uploading their manuscript to self-archive the data in some kind of public repository. But there are many social, political and technical barriers to this, and they have been well documented [8]. You could find out about them in this paper [8], but it appears that the author hasn’t self-archived the paper or taken the “gold” road and pulished in an Open Access journal. Ironic?

Last, but not least, it would be interesting to know what commercial publishers make of all this text-mining magic in Science [9], but we would have to pay $24 to find out. Ironic?

For added ironic amusement, take a screenshot of the offending article and post it to the Flickr group. Sometimes the shame is too much, and articles are retrospectively made open access so a screenshot will preserve the irony.

Join us in poking fun at the crazy business of academic publishing, while making a serious point about the lack of Open Access to scientific data.

* Please note, some research articles in BMJ are available by Open Access, but news articles like [7] are not. Thanks to Trish Groves at BMJ for bringing this to my attention after this blog post was published. Also, some “articles” here are in a grey area for open access, particularly “journalistic” stuff like news, editorials and correspondence, as pointed out by Becky Furlong. See tweets below…

Science Online London (#solo10 September 3-4, 2010) is an annual gathering of people interested in the use of web technologies for scientific collaboration and communication. The organisers at Mendeley, Nature Network and The British Library continue to do a great job of hosting this important gathering, now in its third year:

I’ve been the last two years (2008 and 2009), and it has been worth attending because of the mix speakers, delegates and topics covered. This year includes talks from:

See the impressive full programme here. Reading through the speaker list I wondered, where are all the scientists at science online this year? At the time of writing this, 12 of the 13 speakers are politicians, publishers or journalists with scientist Peter Murray-Rust the odd man out. I’ve nothing against politicians, publishers or journalists but it would be great to have a more balanced event this year. The UK is full of high-profile scientists with blogs who would probably jump at the opportunity to speak at this event. So:

Dear readers of this blog: this gathering is fun, sign up now for the last few tickets

The digitization of libraries had a clear initial goal: to permit anyone to read the contents of collections anywhere and anytime. But universal access is only the beginning of what may happen to libraries and researchers in the digital age. Because machines as well as humans have access to the same online collections, a complex web of interactions is emerging. Digital libraries are now engaging in online relationships with other libraries, with scholars, and with software, often without the knowledge of those who maintain the libraries, and in unexpected ways. These digital relationships open new avenues for discovery, analysis, and collaboration.

Daniel J. Cohen is an Associate Professor at George Mason University and has been involved in the development of the Zotero extension for the Firefox browser that enables users to manage bibliographic data while doing online research. Zotero [1] is one of many new tools [2] that are attempting to add a social dimension to scholarly information on the Web, so this should be an interesting talk.

Last Saturday, The Royal Institution of Great Britain (R.I.) hosted a conference called Science Online London (#solo09) co-organised by mendeley.com and network.nature.com. The event centred around the fantastic Faraday Theatre which according to the R.I. is a “beautiful, historic theatre [which] has deeply raked seating that creates an intimate atmosphere, even when full to capacity”. Absolutely. Just like last year, this event attracted delegates and speakers from a wide range of backgrounds in science, publishing and communication from around the world. This post is an approximately alphabetically ordered link-fest of some of the people involved. People are, after all, the most interesting thing about any conference. If you’re not listed here it’s not because I don’t like you (honest!) it’s because we didn’t speak or I didn’t listen or (unlike many people) you’re not vain enough [1] to have a have a blog (yet) 🙂

Dave Munger, founder of researchblogging.org, gave a presentation with his “blogging optimist” hat on in the blogging for impact session. Dave pointed out that blogs don’t have to be controversial to have an impact, or time consuming, for example posting just once a month can be enough to have an impact. That’s part of the beauty of the pub-sub model of publishing. See Dave’s (telepresent) report.

Daniel MacArthur of The Sanger and Genetic Future. Daniel gave a great talk with his “blogging realist” hat on (to follow on from the blogging optimist talk) in the Blogging for Impact session. Daniel pointed out that there is never enough time to blog everything that is interesting and that time spent blogging is time not spent doing experiments, coding, analysis, grant-writing etc. In the blogosphere (as elsewhere) controversy sells (but this means you can annoy colleagues and peers off in your community). Inacurrate, exaggerated or even perfectly valid criticism can damage careers.

Now I’m told the presentations mentioned above will be on Nature Precedings in due course, which will be good. Thanks to all the organisers, speakers and participants this year that made Science Online London 2009 well worth attending. Hopefully see some more of you again next year!

The latest results from the annual impact factor boxing world championship contest are out. This is a combat sport where scientific journals are scored according to their supposed influence and impact in Science. This years competition rankings include the first-ever update to the newly introduced Five Year Impact Factor and Eigenfactor™ Metrics [1,2] in Journal Citation Reports (JCR) on the Web (see www.isiknowledge.com/JCR warning: clunky website requires subscription*), presumably in response to widespread criticism of impact factors. The Eigenfactor™ seems to correlate quite closely with the impact factor scores, both of which work at the level of the journal, although they use different methods for measuring a given journals impact. However, what many authors are often more interested in is the impact of an individual article, not the journal where it was published. So it would be interesting to see how the figures below tally with Google Scholar, see also comments by Abhishek Tiwari. I’ve included a table below of bioinformatics impact factors, updated for June 2009. Of course, when I say 2009 (today), I mean 2008 (these are the latest figures available based on data from 2007) – so this shiny new information published this week is already out of date [3] and flawed [4,5] but here is a selection of the data anyway: [update: see figures published in June 2010.]

Abstract: The DBLP (Digital Bibliography & Library Project) Computer Science Bibliography now includes more than 1.2 million bibliographic records. For Computer Science researchers the DBLP web site now is a popular tool to trace the work of colleagues and to retrieve bibliographic details when composing the lists of references for new papers. Ranking and profiling of persons, institutions, journals, or conferences is another usage of DBLP. Many scientists are aware of this and want their publications being listed as complete as possible.

The talk focuses on the data acquisition workflow for DBLP. To get ‘clean’ basic bibliographic information for scientific publications remains a chaotic puzzle.

Large publishers are either not interested to cooperate with open services like DBLP, or their policy is very inconsistent. In most cases they are not able or not willing to deliver basic data required for DBLP in a direct way, but they encourage us to crawl their Web sites. This indirection has two main problems:

The organisation and appearance of Web sites changes from time to time, this forces a reimplementation of information extraction scripts. [1]

In many cases manual steps are necessary to get ‘complete’ bibliographic information.

For many small information sources it is not worthwhile to develop information extraction scripts. Data acquisition is done manually. There is an amazing variety of small but interesting journals, conferences and workshops in Computer Science which are not under the umbrella of ACM, IEEE, Springer, Elsevier etc. How they get it often is decided very pragmatically.

The goal of the talk and my visit to Manchester is to start a discussion process: The EasyChair conference management system developed by Andrei Voronkov and DBLP are parts of scientific publication workflow. They should be connected for mutual benefit?

What are the costs and benefits of blogging and how can you make sure the latter justifies the former?

This (proposed) session will look at two kinds of profit, and the costs associated with each.

Research profit (in science and academia), building digital reputations on the Web. Can blogging help your next grant proposal for research funding and if so, how? How can blogging be used to increase the visibility and impact of published research via the likes of ResearchBlogging.org, blogs.nature.com and other aggregators?

Financial profit (in business), making blogging pay the bills. What business models (and infrastructure) exist to support blogging? Including, but not limited to: Nature Network, ScienceBlogs, Google AdSense, “20% time“, “free” tools (WordPress, Blogger, OpenWetWare etc). Going solo vs. joining a club – which business models and tools are right for you?

This could be followed by a general discussion on these benefits. When do they justify their costs (and risks) and make for profitable blogging?

If this is a successful proposal, I’ll need some help. Any offers? If you are interested in joining in the fun, details are at scienceonlinelondon.org